Typing tool
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Typing tool
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Complete norovirus genomes
| PQ304633 | GII.17 | |
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| GII.P17 |
ORF1: 6..5114
ORF2: 5095..6720
ORF3: 6720..7499
LOCUS PQ304633 7554 bp RNA linear VRL 17-OCT-2024
DEFINITION Norovirus GII isolate Hu/GII.17[P17]/SanFrancisco0147/2023/USA,
complete genome.
ACCESSION PQ304633
VERSION PQ304633.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7554)
AUTHORS Chhabra,P., Wong,S., Niendorf,S., Lederer,I., Vennema,H., Faber,M.,
Nisavanh,A., Jacobsen,S., Williams,R., Colgan,A., Yandle,Z.,
Garvey,P., Al-Hello,H., Ambert-Balay,K., Barclay,L., de Graaf,M.,
Celma,C., Breuer,J., Vinje,J. and Douglas,A.
TITLE Increased circulation of GII.17 noroviruses, six European countries
and the United States, 2023 to 2024
JOURNAL Euro Surveill 29 (39) (2024)
REMARK DOI: 10.2807/1560-7917.ES.2024.29.39.2400625
REFERENCE 2 (bases 1 to 7554)
AUTHORS Pan,C.-Y., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (10-SEP-2024) Viral Gastroenteritis Branch, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. v. 11.1.2; SPAdes v. v. 3.6
Sequencing Technology :: Sanger dideoxy sequencing; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7554
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.17[P17]/SanFrancisco0147/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="15-Mar-2023"
/note="genotype: GII.17[P17]"
gene 6..5114
/gene="ORF1"
CDS 6..5114
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XGK29421.1"
/translation="MKMASNDASAAVAGKNNNNDKEKSSSDNLFSNMTVTFKKALGAR
SKQPPPGEVKQTQKPPRPPTPELVKRIPPPPPNGEDGPQIVYKVGEGVSGLPDLTTVT
RPDTQDTAYSVPPLSQREAGEAKEPLPGSILEMWDGEIYHYGLYVERGNVLGVHKPPA
AVSLAKIELTPLSLYWRVVYTPQYLISPDTLKGLSGETFPYTAFDNNCYAFCCWVLDL
NDSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDI
IGKLRPLNILNILATCDWTFAGIVESMILLAELFGVYWTPPDVSAMIAPLLGDYEMQG
PEDLAVELVPVVMGGIGLVLGFTKEKVGKMLSSAATTLRACKDLGSYGLEILKLIMKW
FFPKKEEASELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARK
LSTKSASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMLSGRPGIGKTHLA
RELAKKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELA
DTCPLTLNCDRIENKGKVFDSDVIVITTNLANPAPLDYVNFEACSRRIDFLVYAEAPD
IEKAKRDFPGQPDMWKDHYRPDFTHIKLQLAPQGGFDKNGNTPHGKGVMKSLTVGSLI
ARASGLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSV
KTLDELKQAIKNISIKKCQIVYNGCTYTMESDGRGKVVVEKVQNATVQTNNELTGALH
HLRSARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVKRMNISNLWSKPPVEEGDEPEDK
GGCPKPRDEDDLTIDSKDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREE
RNGKYSIEEYLQDRDRYYEELAIAKAIEEDFCEEEEIKIRQRIFRPTRKQRKEERATL
GLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFW
VSPSLFITSTHVIPKGITEAFGVPMSQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGA
PEGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRMVGGQMGMLLTGSNAKSMDLGTT
PGDCGCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAP
ILGPGSAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPF
TEPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHARKN
DYWNGETFTGKLADQASKANLMYEEGKHMQPVFTAALKDELVKTDKIYGKIKKRLLWG
SDLSTMIRCARAFGGLMDELKANCIALPVRVGMNMNEDGPIIFEKHSRYRYHYDADYS
RWDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGV
PCTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSIYSFYGDDEIVSTDIKLDPEKLTA
KLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQIYWT
RGPNHEDPSETMIPHAQRPVQLMALLGESSLHGPAFYSKVSKLVISELKEGGMDFYVP
RQESMFRWIRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 6..1004
/gene="ORF1"
/product="p48"
mat_peptide 1005..2102
/gene="ORF1"
/product="NTPase"
mat_peptide 2103..2639
/gene="ORF1"
/product="p22"
mat_peptide 2640..3038
/gene="ORF1"
/product="VPg"
mat_peptide 3039..3581
/gene="ORF1"
/product="Pro"
mat_peptide 3582..5111
/gene="ORF1"
/product="RdRp"
gene 5095..6720
/gene="ORF2"
CDS 5095..6720
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XGK29422.1"
/translation="MKMASNDAAPSNDGATGLVPEINTETLPLEPVAGASLAAAVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
VRNTFFHYNNRPSERMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTISELTNSRFPAPIDSLFTAQNNVLNVQCQNGRCTLDGELQGTT
QLLPTGICAFRGKITADVENQHDDRWHLSITNLNGTPFDPTEDVPAPLGTPDFTGLLF
GVASQRNVGGSGNNTTRAHEAVISTTSTQFVPKLGSVNFGSQSDDFQVSQPTKFTPVG
IKIETGHPFEQWRLPNYAGALTLNMNLAPPIAPNFPGEQLLFFRSNIPCAGGISDGVI
DCLLPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRTGYITVAHTGDYPL
VVPSNGFFRFDSWVNQFYSLAPMGTGNGRRRIQ"
gene 6720..7499
/gene="ORF3"
CDS 6720..7499
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XGK29423.1"
/translation="MAGAFIAGLAGDMLTSTVGSLANAGANAINQKIDFENNKQLQAA
SFQHDKDMLLAQVNATKQLQSDMIAIKQGILTAGGFSPTDAARGAVGAPMTKVLDWSG
TRYWAPNSTKTTSYSGQFTSTPVHTPNLSSKPKTTSVKSPSPSSSSGSVYSLATQSTS
LSGPSSGSSASSASTQSTKLSSTSSMSRTIDWVNQQRSLSPYMSGALNISHVTPPSSR
ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV"
ORIGIN
1 tgtgaatgaa gatggcgtct aacgacgctt ccgctgccgt tgctggcaaa aacaacaaca
61 acgacaagga aaaatcttca agtgacaact tgttttctaa catgactgtc acttttaaga
121 aagccctcgg ggcgcggtct aaacagccgc ccccgggaga agtaaaacaa acacagaaac
181 caccaagacc accgacaccg gaattggtga agagaatacc cccaccccca cccaatggcg
241 aggatggacc acaaatagtg tataaggtgg gggagggtgt gtctgggcta cccgacctaa
301 caaccgtgac gcggcctgac acacaagaca cagcttatag tgttcccccg ctaagccaga
361 gagaagccgg cgaagctaaa gaaccactgc ctggttccat tcttgagatg tgggatggtg
421 agatctacca ttatgggctg tatgttgaac ggggaaatgt actcggggtg cacaaaccac
481 ctgctgcagt aagcctcgcc aaaattgaat taacacctct gtctctctac tggagagtgg
541 tatacactcc ccagtatctg atatctccag acactcttaa gggcttgagc ggagagactt
601 tcccatacac ggcctttgat aacaactgct atgccttctg ttgttgggtc ctagacctca
661 atgactcctg gctcagcagg aggatgatcc aaagaacaac tggatttttc agaccgtatc
721 aggattggaa cagaaagcct ttgccaacca tggatgagcc gaaaatcaag aaggccgcaa
781 atgctgtcct ttgtgctctc tcctcactct ttaccagacc cattaaggat atcattggaa
841 aactcaggcc attaaacatc ctcaacattc tggcaacatg tgactggact tttgcaggca
901 tagtggaatc catgatcctt cttgctgaac tctttggggt gtactggact cccccagacg
961 tgtctgcgat gattgctccc ttactcggtg actacgaaat gcaaggcccc gaagacctgg
1021 ccgtggaact tgtgcccgtg gtaatgggag gaataggctt ggtgttagga ttcaccaaag
1081 aaaaggtcgg caagatgctt tcatcagctg caaccacact tagggcctgt aaagacctag
1141 gttcttatgg actggagata ctcaaattaa tcatgaagtg gttcttcccc aagaaggaag
1201 aggctagtga actagccatg gtgagggcca ttgaggatgc agtcctggat ttggaggcga
1261 tagaaaataa ccacatgacc accctcctca aggacaaaga tagcctggcc acatacatga
1321 gaactcttga cttggaggaa gagaaagcaa ggaaactatc aaccaaatcg gcatcacctg
1381 acatcgtggg cacaataaac gcattattgg caaggattgc agctgctagg tcactggtcc
1441 acaaggccaa ggaggagctc tcgagcagac agaggcctgt tgttgtaatg ttatcaggta
1501 gaccaggcat aggaaagacc caccttgcca gagagctagc caagaaagtt gcatctacac
1561 tgtcaggtga ccaaagaatt ggattggtgc ctagaaatgg cgtcgatcac tgggatgcct
1621 acaagggaga aagggtagtc ctgtgggatg actacggtat gagcaaccct atacaggacg
1681 cattgaggct ccaagaattg gctgacacat gcccactaac cctaaattgt gacaggattg
1741 aaaacaaagg aaaagtgttc gacagtgatg tcatagtcat aacaaccaac cttgcaaacc
1801 cagcaccact agattatgtc aactttgagg cctgctctag acgcatagac ttcttggtgt
1861 atgcagaagc acctgacatc gagaaggcta agcgtgattt ccctggccaa ccagatatgt
1921 ggaaagacca ctatagacca gacttcacac acattaaact tcaactggca ccacaaggag
1981 gttttgacaa gaatggtaac accccacatg gcaaaggtgt gatgaagtca ctgacggttg
2041 gttctctgat cgccagggct tctggcttgc tccacgaaag aatggatgaa tttgagctcc
2101 agggctctga cctgccaacc ttcaactttg accgtaacaa agtcgccgcc ttcaggcaat
2161 tggcagctga aaataaatat ggtcttatgg acacactgag ggtcggcaac caactgaaga
2221 gtgtcaaaac cctagatgag ctgaagcagg ccataaagaa catcagcatc aagaagtgcc
2281 aaatagtgta taatggctgt acatacacca tggaatctga tgggaggggc aaggttgtgg
2341 ttgaaaaggt gcaaaatgca acagtccaaa ccaataacga actcacagga gcactccatc
2401 acctgaggtc tgcaaggata agatattatg tcaaatgttt ccaagaagcc atttactcct
2461 tactccaaat cgctggtgca gcctttgtta cttcacgcat cgtgaaacgc atgaacatct
2521 caaatctctg gtcaaaacca cccgtcgaag agggtgatga acctgaagac aaaggaggat
2581 gccctaaacc cagggatgaa gatgacctca ccattgactc taaagacata aaagtggaag
2641 ggaaaaaggg caaaaacaag tctggtcggg gcaagaaaca cacagccttc tcatccaagg
2701 gcctcagtga tgaagagtac gatgagtaca agagaatcag agaggagagg aatggtaaat
2761 actcaataga ggaatacctc caagatagag acagatacta tgaagaactt gccattgcta
2821 aggccattga agaggacttc tgtgaagagg aggaaatcaa aatccgccag agaatcttcc
2881 gacccaccag gaagcaacga aaagaggaga gggccacgct cggactcgtc acaggatcag
2941 aaatcaggaa aagaaaccca gatgacttta aaccaaaagg aaaattgtgg gctgatgaca
3001 acaggagtgt ggattacaat gagagaatag attttgaggc ccccccgagc gtttggtcta
3061 gaatagtcaa ttttggcaca ggttggggat tctgggtttc tccaagtctc tttataactt
3121 caacacatgt cataccaaaa ggaattactg aagcctttgg agtgcccatg agtcaaatcc
3181 agattcacaa atccggagaa ttttgccgct tgcggtttcc aaaaccaatt agaccagacg
3241 tgagtgggat gatcttggaa gagggtgccc ctgaaggcac tgttgtgtct attctcatca
3301 aaaggacaac aggggagctg atgcctcttg cagtcagaat gggaacccat gccacaatga
3361 aaattcaagg tagaatggtg ggtggtcaga tgggtatgct tctcactggt tcaaatgcca
3421 aaagcatgga tttgggtaca acgccaggtg attgcgggtg tccatacatc tacaaaaggg
3481 gcaatgactt cgtggtcatt ggggtgcaca ctgcagcagc acgtggaggc aacacagtca
3541 tatgtgccac acagggaagt gaaggtgagg ccactcttga aggaggtgac aacaagggca
3601 cctactgtgg agcacccatt ctgggacctg gcagtgcacc aaaactgagc acaaaaacaa
3661 aattctggag atcttccaat acgccgcttc ccccaggcac ctatgaacca gcgtaccttg
3721 gtgggagaga cccgcgtgtg aagggaggcc cgtctctgca gcaggttatg agagatcaac
3781 tcaaaccctt tacagaaccc agagggaagc caccaaaccc aaatgtcctg gagtcagcaa
3841 agaagactat tatcaatgtt ttggaacaaa ccatcgaccc ccctcagaag tggtcgtatg
3901 cccaagcttg tgcatctctt gacaaaacga cctccagtgg atacccacac cacgcccgga
3961 agaatgatta ttggaatggt gaaacattca cagggaaact cgcagaccag gcttcaaagg
4021 caaatctcat gtatgaagaa ggcaagcaca tgcaaccagt tttcactgca gcactcaaag
4081 acgagcttgt aaaaactgat aaaatttatg gtaaaatcaa gaaaagactc ctgtggggtt
4141 ctgacctctc caccatgatt cgttgcgcta gagcattcgg tggtctcatg gacgagctta
4201 aagcaaactg cattgcactc cctgtcagag ttggtatgaa tatgaatgaa gatggtccca
4261 taatatttga gaaacactct aggtacagat accactatga tgcagattac tcccgctggg
4321 attccacaca acagcgggca gtgctggaag cggcacttga aattatggtg agattttctg
4381 ctgaaccaca gctggcacaa atagtggcag aggatctgct gtcaccaagt gtggtggatg
4441 tgggcgactt caaaatcgca atcaatgaag gcctaccatc tggtgtgcct tgcacctcac
4501 aatggaactc tattgcccac tggctactca ccctgtgtgc cctttctgaa gtgacaggac
4561 taggccccga catcatacaa gccaactcca tatactcttt ctatggtgat gatgagattg
4621 tgagcacgga cataaaattg gacccagaga aattaactgc aaaactcaaa gaatatggcc
4681 ttaaacccac acggcccgac aaaactgagg gaccgctggt gatcagtgag gacctgaatg
4741 ggttaacatt cctacgccgg acagtgaccc gcgacccagc aggctggttt ggaaaattgg
4801 accaaagttc tatcctcagg cagatttatt ggacaagggg acccaaccat gaagatccca
4861 gtgaaaccat gataccacac gcacagagac ctgtgcagct catggcatta ttaggagaat
4921 cctccctaca tggaccagca ttttacagca aggtcagcaa gctggtcata tctgaactca
4981 aagagggagg aatggatttt tatgtgccca gacaagagtc aatgttcaga tggataaggt
5041 tctcggatct aagcacatgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag
5101 atggcgtcga atgacgccgc tccatctaat gatggtgcta cgggcctcgt cccagagatc
5161 aacaccgaga cccttccttt ggaaccagtg gctggtgcat cccttgcagc agctgtcact
5221 ggtcaaaaca atataattga tccctggatt agaacaaatt ttgtacaagc acccaatggg
5281 gaatttactg tatcacccag aaattcccca ggagagattc ttctaaattt ggaattaggt
5341 cctgatttaa atccttattt ggcacacctg tctagaatgt acaatggcta cgctggcgga
5401 gttgaagtcc aggtgctctt ggcggggaat gcgttcaccg ctggaaagat ccttttcgcc
5461 gctgtgccac caaattttcc agttgaattt cttagtcctg ctcaaataac tatgcttcca
5521 catttgatag ttgatgttag aactcttgag ccaatcatga tacctcttcc tgatgtgaga
5581 aataccttct tccactacaa caaccgtccc tctgagcgca tgcgcttagt ggctatgctg
5641 tatactcctt taagatccaa tggttcaggt gatgatgtct tcacagtctc gtgtagagtt
5701 ttaaccaggc ctaccccaga ctttgagttc acttatttag tcccaccttc agttgaatct
5761 aaaacaaaac ctttttctct ccctatcctg actatctctg agctgaccaa ttcaagattc
5821 ccagcaccta ttgattcact gtttactgct caaaataatg tccttaatgt ccagtgtcaa
5881 aatggccggt gcactctgga tggagagctg caaggaacca cccaattact tccaactgga
5941 atatgtgcct tcaggggaaa gataacagca gatgtagaaa atcagcatga tgacaggtgg
6001 cacttgagta taacaaacct caatggaact ccttttgatc caacagaaga tgtcccagcc
6061 ccattaggca cccctgactt cacaggcctc ctcttcggag ttgcaagcca aagaaatgtc
6121 ggtgggtcag gcaacaacac caccagggca catgaggctg tgatatcaac aaccagcaca
6181 caatttgttc caaaattagg ttctgtcaac tttgggagtc agagtgacga ttttcaggtt
6241 tctcagccaa ctaagttcac accagttggg atcaaaattg aaactggaca cccttttgaa
6301 caatggagat tacccaacta tgctggagca ctgacactta atatgaacct tgccccacct
6361 atcgctccca actttccagg tgagcaattg cttttcttta ggtctaatat cccttgtgct
6421 ggtggtatca gtgacggtgt cattgactgt ctgcttcctc aggagtggat acaacacttc
6481 taccaggagt ctgctccttc tcaatcagat gtggctctaa tcaggtacgt caaccctgac
6541 acgggtcgca ctctctttga ggcgaagctc cacaggaccg gatacatcac tgttgcccac
6601 accggcgatt accctcttgt tgtcccctct aatggcttct tcagatttga ctcttgggta
6661 aaccagtttt actcacttgc ccccatggga actgggaatg ggcgtagaag gattcagtaa
6721 tggcaggagc ttttatagca ggtcttgcag gtgacatgct caccagtact gttggctctc
6781 tggcgaatgc cggagcaaac gccataaacc aaaagataga ctttgagaac aacaaacaat
6841 tgcaagctgc ctctttccaa catgacaaag acatgctcct cgcacaggtg aatgcaacca
6901 aacaactgca gtcagacatg atcgccatca agcaggggat attgaccgcg ggcggctttt
6961 cccctactga tgcagcaagg ggggccgtgg gggcacccat gacaaaagtt ctcgattggt
7021 ctggcactcg ctattgggca ccaaactcca ccaagacaac aagctattca gggcaattca
7081 catcaacgcc tgtgcataca ccaaatttga gtagcaagcc caagaccaca agtgtcaaat
7141 ccccatctcc ttcttcttcc tctggtagtg tttatagtct agcaactcag tcaacttcac
7201 tgtccggacc ttcttcaggt tcctctgctt cttctgcttc aacacaatca acaaaattaa
7261 gctcaacttc ttctatgagt agaacaattg attgggtcaa tcaacaaaga agtctcagcc
7321 catacatgag tggagctctt aacatctccc atgtgacacc tccatcaagt agagcatcta
7381 gttcgggaac agtctcaact gtccccaaag aagttttgga ctcctggaca tctgcattta
7441 acacacacag acagccgctc ttcgcacacc ttagggtaag gggggagtca cgtgtttagt
7501 gaaaagaatt aattagattt aatcaggctt aaatttaatt tgatctttta aaaa
//